Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_8C5-N1-BDNA-1_A23NMNVLT4_1/1136_8C5-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/af/4bd6b71cab453229b87b975af973ab/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_8C5-N1-BDNA-1_A23NMNVLT4_1/1136_8C5-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/foresight/xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/af/4bd6b71cab453229b87b975af973ab/.command.run
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_8C5-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_8C5-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_8C5-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_8C5-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Reads: 69438712 total, 52350 skipped (flags/unmapped)
Fragments: 34775701 total (34580513 tlen-paired, 2784 hash-paired, 328 singletons, 11426 discordant, 180650 orphans, 7969 too large [>5000 bp], 10121209 duplicates)
Reads: 75253218 total, 45860 skipped (flags/unmapped)
Fragments: 37687788 total (37493516 tlen-paired, 2439 hash-paired, 299 singletons, 7977 discordant, 183557 orphans, 7819 too large [>5000 bp], 10790905 duplicates)
Reads: 75232203 total, 48330 skipped (flags/unmapped)
Fragments: 37680061 total (37469384 tlen-paired, 4395 hash-paired, 258 singletons, 9841 discordant, 196183 orphans, 10096 too large [>5000 bp], 11125894 duplicates)
Reads: 82417244 total, 77670 skipped (flags/unmapped)
Fragments: 41327427 total (40839425 tlen-paired, 1962 hash-paired, 319 singletons, 92744 discordant, 392977 orphans, 39008 too large [>5000 bp], 12233847 duplicates)